AssemblyQC

AssemblyQC is a Nextflow pipeline which evaluates assembly quality with well established tools and presents the results in a unified html report.

Reference:

Rashid, U., Wu, C., Shiller, J., Smith, K., Crowhurst, R., Davy, M., Chen, T.-H., Thomson, S., & Deng, C. (2024). AssemblyQC: A NextFlow pipeline for evaluating assembly quality (1.4). Zenodo. 10.5281/zenodo.10647870. GitHub. https://github.com/Plant-Food-Research-Open/assemblyqc

Pipeline Parameters

Only displaying parameters that differ from the pipeline defaults.

{
    "runName": "marvelous_hugle",
    "containerEngine": "apptainer",
    "launchDir": "/powerplant/workspace/hrasrb/Repo/assembly_qc",
    "workDir": "/powerplant/workspace/hrasrb/Repo/assembly_qc/work",
    "projectDir": "/powerplant/workspace/hrasrb/Repo/assembly_qc",
    "userName": "hrasrb",
    "profile": "pfr,apptainer",
    "input": "/powerplant/workspace/hrasrb/Repo/assembly_qc/pfr/assemblysheet_hrasrb.csv",
    "outdir": "./cleaned_blueberry_haplotype_results",
    "ncbi_fcs_adaptor_empire": "euk",
    "ncbi_fcs_gx_tax_id": "3750",
    "ncbi_fcs_gx_db_path": "/workspace/ComparativeDataSources/NCBI/FCS/GX/r2023-01-24",
    "busco_skip": "false",
    "busco_mode": "geno",
    "busco_lineage_datasets": "embryophyta_odb10 eudicots_odb10",
    "busco_download_path": "/workspace/ComparativeDataSources/BUSCO/assemblyqc",
    "tidk_skip": "false",
    "tidk_repeat_seq": "TTTAGGG",
    "lai_skip": "false",
    "kraken2_db_path": "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314",
    "synteny_xref_assemblies": "/workspace/assemblyqc/testdata/default/xrefsheet.csv",
    "config_profile_name": "Plant&Food profile",
    "config_profile_description": "Plant&Food profile using SLURM in combination with Apptainer"
}

Pipeline Tools

Following is a non-exhaustive list of tools used to generate this report.

{
    "LTR_FINDER_parallel": "v1.1",
    "LTR_HARVEST_parallel": "v1.1",
    "LTR_retriever": "v2.9.9",
    "Nextflow": "23.04.4",
    "assemblathon_stats": "github/PlantandFoodResearch/assemblathon2-analysis/a93cba2",
    "biopython": "1.75",
    "busco": "5.6.1",
    "genometools": "1.6.5",
    "lai": "beta3.2",
    "ltr_finder": "v1.07",
    "pigz": "2.3.4",
    "plant-food-research-open/assemblyqc": "1.4",
    "py_fasta_validator": "0.6",
    "python": "3.8.13",
    "seqkit": "v2.6.1",
    "tidk": "0.2.41",
    "yaml": "5.4.1"
}

A script to calculate a basic set of metrics from a genome assembly.

Reference:

https://github.com/KorfLab/Assemblathon

Version: github/PlantandFoodResearch/assemblathon2-analysis/a93cba2

Warning:

Contig-related stats are based on the assumption that the assemblathon_stats_n_limit (100) parameter is specified correctly. If you are not certain of the value of the n_limit parameter, please ignore the contig-related stats.

M7_hap1_clean

Stat	Value
Assembly	classified_M7_plus_unclassified_hap1.clean.fa
Number of scaffolds	412
Total size of scaffolds	531169080
Longest scaffold	14681403
Shortest scaffold	15542
Number of scaffolds > 1K nt	412
Percentage of scaffolds > 1K nt	100.0
Number of scaffolds > 10K nt	412
Percentage of scaffolds > 10K nt	100.0
Number of scaffolds > 100K nt	259
Percentage of scaffolds > 100K nt	62.9
Number of scaffolds > 1M nt	121
Percentage of scaffolds > 1M nt	29.4
Number of scaffolds > 10M nt	6
Percentage of scaffolds > 10M nt	1.5
Mean scaffold size	1289245
Median scaffold size	245799
N50 scaffold length	5202741
L50 scaffold count	34
scaffold %A	30.74
scaffold %C	19.27
scaffold %G	19.27
scaffold %T	30.72
scaffold %N	0.0
scaffold %non-ACGTN	0.0
Number of scaffold non-ACGTN nt	0
Percentage of assembly in scaffolded contigs	0.0
Percentage of assembly in unscaffolded contigs	100.0
Average number of contigs per scaffold	1.0
Mean length of breaks (>=100Ns) between contigs in scaffold	0
Number of contigs	412
Number of contigs in scaffolds	0
Number of contigs not in scaffolds	412
Total size of contigs	531169080
Longest contig	14681403
Shortest contig	15542
Number of contigs > 1K nt	412
Percentage of contigs > 1K nt	100.0
Number of contigs > 10K nt	412
Percentage of contigs > 10K nt	100.0
Number of contigs > 100K nt	259
Percentage of contigs > 100K nt	62.9
Number of contigs > 1M nt	121
Percentage of contigs > 1M nt	29.4
Number of contigs > 10M nt	6
Percentage of contigs > 10M nt	1.5
Mean contig size	1289245
Median contig size	245799
N50 contig length	5202741
L50 contig count	34
contig %A	30.74
contig %C	19.27
contig %G	19.27
contig %T	30.72
contig %N	0.0
contig %non-ACGTN	0.0
Number of contig non-ACGTN nt	0

Stat	Value
Assembly	classified_M7_plus_unclassified_hap2.clean.fa
Number of scaffolds	378
Total size of scaffolds	522235882
Longest scaffold	17018523
Shortest scaffold	16806
Number of scaffolds > 1K nt	378
Percentage of scaffolds > 1K nt	100.0
Number of scaffolds > 10K nt	378
Percentage of scaffolds > 10K nt	100.0
Number of scaffolds > 100K nt	263
Percentage of scaffolds > 100K nt	69.6
Number of scaffolds > 1M nt	117
Percentage of scaffolds > 1M nt	31.0
Number of scaffolds > 10M nt	8
Percentage of scaffolds > 10M nt	2.1
Mean scaffold size	1381576
Median scaffold size	297909
N50 scaffold length	5120845
L50 scaffold count	31
scaffold %A	30.73
scaffold %C	19.29
scaffold %G	19.28
scaffold %T	30.69
scaffold %N	0.0
scaffold %non-ACGTN	0.0
Number of scaffold non-ACGTN nt	0
Percentage of assembly in scaffolded contigs	0.0
Percentage of assembly in unscaffolded contigs	100.0
Average number of contigs per scaffold	1.0
Mean length of breaks (>=100Ns) between contigs in scaffold	0
Number of contigs	378
Number of contigs in scaffolds	0
Number of contigs not in scaffolds	378
Total size of contigs	522235882
Longest contig	17018523
Shortest contig	16806
Number of contigs > 1K nt	378
Percentage of contigs > 1K nt	100.0
Number of contigs > 10K nt	378
Percentage of contigs > 10K nt	100.0
Number of contigs > 100K nt	263
Percentage of contigs > 100K nt	69.6
Number of contigs > 1M nt	117
Percentage of contigs > 1M nt	31.0
Number of contigs > 10M nt	8
Percentage of contigs > 10M nt	2.1
Mean contig size	1381576
Median contig size	297909
N50 contig length	5120845
L50 contig count	31
contig %A	30.73
contig %C	19.29
contig %G	19.28
contig %T	30.69
contig %N	0.0
contig %non-ACGTN	0.0
Number of contig non-ACGTN nt	0

Stat	Value
Assembly	classified_Nui_plus_unclassified_hap1.clean.fa
Number of scaffolds	774
Total size of scaffolds	522862822
Longest scaffold	19924815
Shortest scaffold	12307
Number of scaffolds > 1K nt	774
Percentage of scaffolds > 1K nt	100.0
Number of scaffolds > 10K nt	774
Percentage of scaffolds > 10K nt	100.0
Number of scaffolds > 100K nt	341
Percentage of scaffolds > 100K nt	44.1
Number of scaffolds > 1M nt	114
Percentage of scaffolds > 1M nt	14.7
Number of scaffolds > 10M nt	6
Percentage of scaffolds > 10M nt	0.8
Mean scaffold size	675533
Median scaffold size	72322
N50 scaffold length	4551404
L50 scaffold count	34
scaffold %A	30.79
scaffold %C	19.21
scaffold %G	19.22
scaffold %T	30.78
scaffold %N	0.0
scaffold %non-ACGTN	0.0
Number of scaffold non-ACGTN nt	0
Percentage of assembly in scaffolded contigs	0.0
Percentage of assembly in unscaffolded contigs	100.0
Average number of contigs per scaffold	1.0
Mean length of breaks (>=100Ns) between contigs in scaffold	0
Number of contigs	774
Number of contigs in scaffolds	0
Number of contigs not in scaffolds	774
Total size of contigs	522862822
Longest contig	19924815
Shortest contig	12307
Number of contigs > 1K nt	774
Percentage of contigs > 1K nt	100.0
Number of contigs > 10K nt	774
Percentage of contigs > 10K nt	100.0
Number of contigs > 100K nt	341
Percentage of contigs > 100K nt	44.1
Number of contigs > 1M nt	114
Percentage of contigs > 1M nt	14.7
Number of contigs > 10M nt	6
Percentage of contigs > 10M nt	0.8
Mean contig size	675533
Median contig size	72322
N50 contig length	4551404
L50 contig count	34
contig %A	30.79
contig %C	19.21
contig %G	19.22
contig %T	30.78
contig %N	0.0
contig %non-ACGTN	0.0
Number of contig non-ACGTN nt	0

Stat	Value
Assembly	classified_Nui_plus_unclassified_hap2.clean.fa
Number of scaffolds	483
Total size of scaffolds	532617838
Longest scaffold	13744249
Shortest scaffold	15236
Number of scaffolds > 1K nt	483
Percentage of scaffolds > 1K nt	100.0
Number of scaffolds > 10K nt	483
Percentage of scaffolds > 10K nt	100.0
Number of scaffolds > 100K nt	313
Percentage of scaffolds > 100K nt	64.8
Number of scaffolds > 1M nt	134
Percentage of scaffolds > 1M nt	27.7
Number of scaffolds > 10M nt	6
Percentage of scaffolds > 10M nt	1.2
Mean scaffold size	1102728
Median scaffold size	212237
N50 scaffold length	3832205
L50 scaffold count	38
scaffold %A	30.77
scaffold %C	19.23
scaffold %G	19.23
scaffold %T	30.77
scaffold %N	0.0
scaffold %non-ACGTN	0.0
Number of scaffold non-ACGTN nt	0
Percentage of assembly in scaffolded contigs	0.0
Percentage of assembly in unscaffolded contigs	100.0
Average number of contigs per scaffold	1.0
Mean length of breaks (>=100Ns) between contigs in scaffold	0
Number of contigs	483
Number of contigs in scaffolds	0
Number of contigs not in scaffolds	483
Total size of contigs	532617838
Longest contig	13744249
Shortest contig	15236
Number of contigs > 1K nt	483
Percentage of contigs > 1K nt	100.0
Number of contigs > 10K nt	483
Percentage of contigs > 10K nt	100.0
Number of contigs > 100K nt	313
Percentage of contigs > 100K nt	64.8
Number of contigs > 1M nt	134
Percentage of contigs > 1M nt	27.7
Number of contigs > 10M nt	6
Percentage of contigs > 10M nt	1.2
Mean contig size	1102728
Median contig size	212237
N50 contig length	3832205
L50 contig count	38
contig %A	30.77
contig %C	19.23
contig %G	19.23
contig %T	30.77
contig %N	0.0
contig %non-ACGTN	0.0
Number of contig non-ACGTN nt	0

BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs.

Reference:

Manni M., Berkeley M.R., Seppey M., Simao F.A., Zdobnov E.M. 2021. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. arXiv:2106.11799 [q-bio] [Internet]. Available from: arxiv.org/abs/2106.11799

Version: 5.6.1

Summary

Assembly	Lineage	Percentages
M7_hap1_clean	eudicots_odb10	C:95.6%[S:88.5%,D:7.1%],F:1.0%,M:3.4%,n:2326
M7_hap1_clean	embryophyta_odb10	C:96.9%[S:89.8%,D:7.1%],F:1.1%,M:2.0%,n:1614
M7_hap2_clean	embryophyta_odb10	C:96.3%[S:89.9%,D:6.4%],F:0.9%,M:2.8%,n:1614
M7_hap2_clean	eudicots_odb10	C:94.9%[S:88.2%,D:6.7%],F:1.0%,M:4.1%,n:2326
Nui_hap1_clean	eudicots_odb10	C:93.8%[S:87.4%,D:6.4%],F:1.2%,M:5.0%,n:2326
Nui_hap1_clean	embryophyta_odb10	C:95.5%[S:89.1%,D:6.4%],F:1.2%,M:3.3%,n:1614
Nui_hap2_clean	eudicots_odb10	C:94.9%[S:87.7%,D:7.2%],F:1.0%,M:4.1%,n:2326
Nui_hap2_clean	embryophyta_odb10	C:96.5%[S:89.7%,D:6.8%],F:0.9%,M:2.6%,n:1614

Event	Frequency
Complete BUSCOs (C)	2224
Complete and single-copy BUSCOs (S)	2058
Complete and duplicated BUSCOs (D)	166
Fragmented BUSCOs (F)	23
Missing BUSCOs (M)	79
Total BUSCO groups searched	2326

Dependency	Version
hmmsearch	3.1
bbtools	39.01
metaeuk	6.a5d39d9

Event	Frequency
Complete BUSCOs (C)	1565
Complete and single-copy BUSCOs (S)	1450
Complete and duplicated BUSCOs (D)	115
Fragmented BUSCOs (F)	18
Missing BUSCOs (M)	31
Total BUSCO groups searched	1614

Dependency	Version
hmmsearch	3.1
bbtools	39.01
metaeuk	6.a5d39d9

Event	Frequency
Complete BUSCOs (C)	1554
Complete and single-copy BUSCOs (S)	1451
Complete and duplicated BUSCOs (D)	103
Fragmented BUSCOs (F)	15
Missing BUSCOs (M)	45
Total BUSCO groups searched	1614

Parameter	Value
Version	5.6.1
Lineage create on	2024-01-08
mode	euk_genome_met
predictor	metaeuk

Event	Frequency
Complete BUSCOs (C)	2206
Complete and single-copy BUSCOs (S)	2051
Complete and duplicated BUSCOs (D)	155
Fragmented BUSCOs (F)	24
Missing BUSCOs (M)	96
Total BUSCO groups searched	2326

Event	Frequency
Complete BUSCOs (C)	2183
Complete and single-copy BUSCOs (S)	2034
Complete and duplicated BUSCOs (D)	149
Fragmented BUSCOs (F)	28
Missing BUSCOs (M)	115
Total BUSCO groups searched	2326

Event	Frequency
Complete BUSCOs (C)	1542
Complete and single-copy BUSCOs (S)	1438
Complete and duplicated BUSCOs (D)	104
Fragmented BUSCOs (F)	19
Missing BUSCOs (M)	53
Total BUSCO groups searched	1614

Event	Frequency
Complete BUSCOs (C)	2207
Complete and single-copy BUSCOs (S)	2039
Complete and duplicated BUSCOs (D)	168
Fragmented BUSCOs (F)	24
Missing BUSCOs (M)	95
Total BUSCO groups searched	2326

Event	Frequency
Complete BUSCOs (C)	1556
Complete and single-copy BUSCOs (S)	1447
Complete and duplicated BUSCOs (D)	109
Fragmented BUSCOs (F)	14
Missing BUSCOs (M)	44
Total BUSCO groups searched	1614

Assembly	Results
M7_hap1_clean	Intact: 0.0546, Total: 0.3175, Raw LAI: 17.21, LAI: 19.75
M7_hap2_clean	Intact: 0.0557, Total: 0.3086, Raw LAI: 18.03, LAI: 20.79
Nui_hap1_clean	Intact: 0.0546, Total: 0.3000, Raw LAI: 18.20, LAI: 21.29
Nui_hap2_clean	Intact: 0.0576, Total: 0.3158, Raw LAI: 18.25, LAI: 21.05